In the process of energy production, mitochondrial networks are key elements to allow metabolism of substrates into ATP. Many pathological conditions have been associated with mitochondrial dysfunction as mitochondria are associated with a wide range of cellular processes. Therefore, any disruption in the energy production induces devastating effects that can ultimately lead to cell death due to chemical ischemia. To address the mitochondrial health and function, there are several bioenergetic parameters reflecting either whole mitochondrial functionality or individual mitochondrial complexes. Particularly, metabolism of nutrients in the tricarboxylic acid cycle provides substrates used to generate electron carriers (nicotinamide adenine dinucleotide [NADH] and flavin adenine dinucleotide [FADH2]) which ultimately donate electrons to the mitochondrial electron transport chain. The levels of NADH and FADH2 can be estimated through imaging of NADH/NAD(P)H or FAD autofluorescence. This report demonstrates how to perform and analyze NADH/NAD(P)H and FAD autofluorescence in a time-course-dependent manner and provides information about NADH and FAD redox indexes both reflecting the activity of the mitochondrial electron transport chain (ETC). Furthermore, total pools of NADH and FAD can be estimated providing information about the rate of substrate supply into the ETC. Finally, the analysis of NADH autofluorescence after induction of maximal respiration can offer information about the pentose phosphate pathway activity where glucose can be alternatively oxidized instead of pyruvate.